vcf2lineage

galaxy-interface-workflow-automation/main-workflow

Author(s)
Wolfgang Maier
Version
1
Last updated
Jun 8, 2021
License
MIT
Tags
variant-analysis
galaxy-interface

Features
Tutorial
Automating Galaxy workflows using the command line
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00079
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Collection\nVariant calls"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nmin-AF for consensus variant"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Dataset\nReference genome"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Compose text parameter value"];
  1 -->|output| 3;
  4["SnpSift Filter"];
  3 -->|out1| 4;
  0 -->|output| 4;
  ee67c5ed-ff7c-404b-ad20-19259edbc671["Output\nconsensus_variants"];
  4 --> ee67c5ed-ff7c-404b-ad20-19259edbc671;
  style ee67c5ed-ff7c-404b-ad20-19259edbc671 stroke:#2c3143,stroke-width:4px;
  5["bcftools consensus"];
  4 -->|output| 5;
  2 -->|output| 5;
  9028f80e-4112-40d8-9a49-f671677d304f["Output\nconsensus"];
  5 --> 9028f80e-4112-40d8-9a49-f671677d304f;
  style 9028f80e-4112-40d8-9a49-f671677d304f stroke:#2c3143,stroke-width:4px;
  6["Collapse Collection"];
  5 -->|output_file| 6;
  1dd7978e-b907-42d6-8fc4-f6fadeefcad1["Output\nmultisample_consensus_fasta"];
  6 --> 1dd7978e-b907-42d6-8fc4-f6fadeefcad1;
  style 1dd7978e-b907-42d6-8fc4-f6fadeefcad1 stroke:#2c3143,stroke-width:4px;
  7["Pangolin"];
  6 -->|output| 7;
  e02d2cfb-9842-4069-957c-6cf4ec197056["Output\npangolin_results"];
  7 --> e02d2cfb-9842-4069-957c-6cf4ec197056;
  style e02d2cfb-9842-4069-957c-6cf4ec197056 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset collection Variant calls
Input parameter min-AF for consensus variant
Input dataset Reference genome

Outputs

From Output Label
Input parameter min-AF for consensus variant
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 SnpSift Filter
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10 bcftools consensus
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 Collapse Collection
toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8 Pangolin

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 486585510 2021-05-28 10:16:46 add WF automation tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows